2.2. 8-10 Proteins [updated]

Question 1

What are amino acids?

Answer 1

Monomers of all proteins, and all amino acids have the same basic structure

Question 2

What is a peptide bond?

Answer 2

a bond formed when two amino acids are joined by a condensation reaction

Question 3

What functions do the properties of proteins give them?

Answer 3

1. Form structural components of animals in particular for example, muscles are made of proteins
2. Their tendency to adopt specific shapes makes proteins important as enzymes, antibodies and some hormones
3. Membranes have proteins constituents that act as carriers and pores for active transport across the membrane and facilitated diffusion

Question 4

What are essential amino acids?

Answer 4

Animals can make some amino acids but must ingest the others.

Question 5

Plants can make all the amino acids they need but only when… ?

Answer 5

If they can access fixed nitrogen such as nitrate

Question 6

What does each amino acid contain?

Answer 6

1. Amino group (-NH2)
2. Carboxyl group (-COOH) on the other end
3. R Group + H

Question 7

What is the simplistic amino acid?

Answer 7

Glycine

Question 8

What enzymes break peptide bonds during digestion?

Answer 8

Protease, they also break down protein hormones so that their effects are not permanent

Question 9

How can an amino acid act as a buffer?

Answer 9

1. Carobxyl group can ionise
2. Amino group can accept an H+ ion
3. At low pH the amino acid will accept H+
4. At high pH, the amino acid will release H+ ions which means it has acidic and base properties

Question 10

What is a primary structure?

Answer 10

the sequence of amino acids found in a molecule

Question 11

What is the secondary structure?

Answer 11

• The coiling or folding of an amino acid chain, which arises often as a result of hydrogen bond formation between different parts of the chain.
• The main forms of secondary structure are the helix and the pleated sheet.

Question 12

What is the tertiary structure?

Answer 12

• The overall three-dimensional shape of a protein molecule. It’s shape arises due to interactions including hydrogen bonding, sulfide bridges, ionic bonds and hydrophobic interactions.

Question 13

What is a quaternary structure?

Answer 13

It is a protein structure where a protein consists of more than one polypeptide chain. For example, insulin.

Question 14

How many amino acids are there?

Answer 14

20. There is a 20^100 possible ways of ordering 100 amino acids

Question 15

How is the helix held of a secondary structure?

Answer 15

Hydrogen bonding between the -NH group of one amino acid and the -CO of the other

Question 16

How is a β-pleated sheet formed in a secondary structure?

Answer 16

When chains in a zig zag structure fold over on itself.

Question 17

What makes the alpha helix and beta pleated sheet stable?

Answer 17

Although weak, many hydrogen bonds.

Question 18

Where do the hydrogen bonds form

Answer 18

Between the hydroxyl, carboxyl and amino groups

Question 19

Where do the Ionic bonds form?

Answer 19

Between those carboxyl and amino groups

Question 20

What is the strongest bond, hydrogen bond, Ionic bond or Disulfide links (covalent)?

Answer 20

Strongest: Disulfide bonding
Then: Ionic bonding
Weakest: Hydrogen bonding

Question 21

Where are disulfide links formed?

Answer 21

Disulfide bridges are formed between the R groups of two cysteines

Question 22

What is a fibrous protein?

Answer 22

Has a relatively long, thin structure it is insoluble in water and metabolically inactive, often having a structural role within an organism e.g collagen.

Question 23

Collagen

Answer 23

Function:
To provide mechanical strength

Found:

• In Artery walls to prevent from bursting (high pressure from blood)
• In tendons - allows them to pull on bones
• In Bones - reinforced with calcium phosphate
• Cartilage and connective tissues

Question 24

Keratin

Answer 24

Function:
Mechanical protection but also provides an impermeable barrier to infection and being waterproof prevents entry of water-borne diseases.

Structure:
- Rich in cysteine –> Loads of di-sulfide bridges form between polypeptide chains. + Hydrogen bonding —> EVEN STRONGER molecule

Found:
Where ever the body parts needs to be hard and strong e.g:
Finger nails, hair, claws, horns, fur and feathers

Question 25

Elastin

Answer 25

Function:
Helps our blood vessels to stretch and recoil as blood is pumped through them, helping maintain the pressure wave of blood as it passes through

Structure:
Cross-linking and coiling make the structure of elastin strong and extensible.

Found:
Living things where they need to stretch to adapt their shape as part of life processes.
-Skin, can stretch around our bones and muscles because of elastin. Without it the skin would not return to normal if you were to pinch it.
- Lungs, allowing them to inflate and deflate
- Bladder, expands to hold urine

Question 26

What is a globular protein?

Answer 26

• Has molecules of a relatively spherical shape, which are soluble in water and often have metabolic roles within organisms
• Hydrophilic groups always on the outside making it water soluble.
• Specific shapes that help them take up roles as enzymes, hormones

Question 27

What is Haemoglobin

Answer 27

Structure:

• Quaternary structure of four polypeptides
• 2 a-globin and 2 b-globin chains
• The interactions between the polypeptide chains give it a specific shape
• Space within the Haemoglobin called the haem group
• Spaces like these are called the Prosthetic group
• Made of Iron ion
• Protein associated with this type of group is called a conjugated protein.

Functions:

• Carry oxygen from the lungs to the tissues.
• Oxygen molecule binds to the iron in each of the four haem groups.
• When it binds the hemoglobin turns from a purple red colour to bright red
• Oxygen is release by the haemoglobin when it reaches the tissues

Question 28

What is Insulin?

Answer 28

Structure:

• 2 Polypeptide chains
• Starts of with the A chain called a-helix and ends with a B chain made of b-pleated sheet.
• Both chains fold into a tertiary structure, then joined by di-sulfide links.
• Amino acids with a hydrophilic R groups are on the outside, which makes the molecule soluble in water.

Function:
- Binds to glycoprotein receptors on the outside of muscle and fat cells to increase their uptake of glucose from the blood, and to increase their consumption of glucose

Question 29

What is Pepsin?

Answer 29

Structure:

• 43 amino acids with acidic R groups
• Four with basic R groups
• Stable in acidic environments of the stomach
• Held by hydrogen bonding and 2 di sulfide bridges

Function:
Enzyme that digests protein in the stomach

Question 30

Ab initio protein modelling

Answer 30

• Model built on physical and electrical properties of the atoms in each amino acid in the sequence.
• With this technique there can be multiple solutions to the same amino acid sequence and other methods sometimes need applying to reduce the number of solutions

Question 31

Comparative protein modelling

Answer 31

• Protein threading, which scans the amino acid sequence against a database of solved structures and produces a set of possible models which would match that sequence