B1.2 Proteins HL

Question 1

what clusters in the core of a globular protein?

Answer 1

hydrophobic amino acids

Question 2

give examples of important amino acids and state whether they are hydrophobic or hydrophilic

Answer 2

• Glutamic acid (hydrophilic)
• Vallne (hydrophobic)
  
  • sickle cell anaemia: one diff base changes glutamic acid to vallne, hydrophilic to hydrophobic
• Cysteine (hydrophobic) → contains sulphur *only amino acid
• Methlonine (hydrophobic)

Question 3

what are used in membrane channels?

Answer 3

polar and non-polar amino acids

Question 4

explain how polar and non-polar amino acids are used in membrane channels

Answer 4

-polar amino acids are positions on external surfaces and line the protein channels for facilitated diffusion

• polar sections allow ions through (charged or polar molecules cannot normally pas through the hydrophobic layers)
• non-polar sections bond with hydrophobic tails

Question 5

what are the 4 structures in protein folding and state the order

Answer 5

Primary structure 1° → Secondary structure 2° → Tertiary structure 3° → Quaternary structure 4°

Question 6

what is the process when a protein goes from secondary structure to primary structure, and is it easy or hard compared tertiary structure to secondary structure

Answer 6

denaturation

sec to pri: hard because a lot of energy is needed to break hydrogen bonds

ter to sec is easier than sec to pri

Question 7

what is primary structure of protein

Answer 7

the unfolded chain of polypeptide

Question 8

what is secondary structure of protein

Answer 8

repeating local structures, held by H-holds

repeating units

• α-helix (hydrogen bonds)
• β-pleated sheets

Question 9

what is tertiary structure of protein?

state and explain the features

Answer 9

3D folded structure

• folding of a single protein into a 3D structure
• hydrophobic core
• this 3D structure gives proteins their functional properties, such as active sites on enzymes
• R group interactions: the below are all dependent on the R-group
  
  • hydrophilic polar amino acids orient to the outside
  • hydrophobic non-polar amino acids protected in the core
  • oppositely-charged ions attract (ionic bond)
  • disulphide bridges globular protein

Question 10

what is the quaternary structure of proteins?

Answer 10

• multiple subunits
• protein complex
• made of two or more subunits

Question 10

what are R group interactions and give examples of R group interactions in tertiary structure

Answer 10

the below are all dependent on the R-group

• hydrophilic polar amino acids orient to the outside
  
  • hydrophobic non-polar amino acids protected in the core
  • oppositely-charged ions attract (ionic bond)
  • disulphide bridges globular protein

Question 10

give an example of quaternary structure of proteins

Answer 10

e.g. haemoglobin, bc it needs to bind onto iron? or oxygen; 4 haem inside contains iron;; (beta chain & alpha chain on outside, haem on inside)

e.g. DNA Polymerase

e.g. Ion channels in the plasma membrane

Question 11

what is temperature sensitive?

Answer 11

hydrogen bonds

hydrogen bonds are very weak → heat a little and it will break → but reforms very easily

Question 12

what is pH sensitive? why?

Answer 12

ionic bonds

if make pH more acidic = add more H+ protons

Question 13

what cannot reform is disulphide bridges are broken?

Answer 13

cysteine cannot reform

(a type of amino acid)

Question 14

denaturation is mostly irreversible, why?

Answer 14

• if in water, if broken into primary structure
• water react to inside of protein → does not want to fold back into original shape

Question 15

what are the 2 types of quaternary structure in protein

Answer 15

non-conjugated and conjugated

Question 16

give examples of non-conjugated quaternary structure of protein

Answer 16

insulin, collagen

Question 17

give examples of conjugated quaternary structure of protein

Answer 17

haemoglobin have 4 polypeptide chain + 4 haem groups

Question 18

how do conjugated and non-conjugated quaternary structure of protein differ?

Answer 18

Non-conjugated only have polypeptide chain

Conjugated have non-polypeptide component (e.g. haem)

Question 19

Describe the structure of insulin

Answer 19

polypeptide chains are separate, but held together using disulphide bridges from R group (cystine)

Question 20

describe the structure of collagen

Answer 20

• quaternary structure = 3 polypeptides, wound together into a triple helix
• fibrous protein → more structural role
• repeating amino acid unit
• primary structure of polypeptides = repeating sequence of 3 amino acids: P-G-X
  
  • can’t change P or G or else will fold differently)
• P = proline
• G = glycine
• X → R group

Question 21

why does collagen have to have amino acid P and G?

Answer 21

• P = proline/hydroxyproline
  
  • prevents formation of an α-helix
  • winding together of 3 polypeptides would be impossible if they were α-helices
• R group is every 3rd amino acid faces inwards towards the centre of the triple helix and glycine is the only amino acid with an R-group small enough to fit → single hydrogen atom

Question 22

if many repeats in bases what does it indicate about the protein?

Answer 22

fibrous protein instead of globular