Unit 2: Section 1 - Biological Molecules

Question 1

How is a dipeptide formed?

Answer 1

A **dipeptide **is formed when **two **amino acids join together.

Question 2

How is a polypeptide formed?

Answer 2

A **polypeptide **is formed when **more than two **amino acids join together.

Question 3

What are proteins made up of?

Answer 3

Proteins are made up of **one **or more polypetides (long chains of amino acids).

Question 4

All amino acids have the same general structure. What does this consist of?

Answer 4

All amino acids have the same general structure - a **carboxyl group **(-COOH) and an **amino/amine group **(-NH₂) attatched to a **carbon **atom.

Question 5

What is the difference between different amino acids?

Answer 5

The **difference **between different amino acids is the variable group (show as a “R” on diagrams) that they contain.

Question 6

Draw the structure of an amino acid (with appropriate labels).

Answer 6

Question 7

1. What is Glycine?
2. What is Glycine’s variable/ “R” group?
3. Draw the structure of Glycine (with appropriate labels).

Answer 7

1. Glycine is the smallest amino acid.
2. The variable/ “R” group of Glycine is a hydrogen atom.
   3.

Question 8

1. What are amino acids joined together by and what does this form?
2. What is released during the reaction? What is the type of reaction?
3. What happens in the reverse of the reaction (in question 2)? What is type of reaction called?

Answer 8

1. Amino acids are linked together by **peptide bonds **to form dipeptides and polypeptides.
2. A molecule of **water **is **released **during the reaction. This type of reaction is a Condensation reaction.
3. The **reverse **of this reaction **adds **a molecule of water to **break **the peptide bond. This is called a hydrolysis reaction.

Question 9

Draw a diagram (with appropriate lablels) of two amino acids joining together to form a dipeptide - including the type of bond being formed.

Answer 9

Question 10

Proteins have four structural levels. One of these is their Primary Structure. Explain the term Primary Structure.

Answer 10

Primary Structure - this is the sequence of amino acids in the polypeptide chain.

Question 11

Proteins have four structural levels. One of these is their Secondary Structure. Explain the term Secondary Structure.

Answer 11

_Secondary Structure _- the polypeptide chain doesn’t remain flat and straight. Hydrogen bonds form between the amino acids in the chain. This makes it automatically coil into an alpha (α) helix or fold into a beat (β) pleated sheet - this is the secondary structure.

Question 12

Proteins have four structural levels. One of these is their Tertiary Structure. Explain the term Tertiary Structure.

Answer 12

_Tertiary Structure _- the coiled or folded chain of amino acids is often **coiled **or folded further. More bonds form between different parts of the polypeptide chain. For proteins made from a **single **polypeptide chain, the tertiary structure forms their final 3D structure.

Question 13

Proteins have four structural levels. One of these is their Quaternary Structure. Explain the term Quaternary Structure.

Answer 13

_Quaternary Structure _- some proteins are made of **several different polypeptide chains **held together by bonds. The quaternary structure is the way these polypeptide chains are assembled together. E.g. **haemoglobin **is made of **four **polypeptide chains, bonded together. For proteins made from **more than one **polypetide chain, the quaternary strucutre is the protein’s final 3D structure.

Question 14

The four structural levels of a protein are held together by different kinds of bonds. Explain the bonds that hold the Primary Structure together.

Answer 14

_Primary Structure _- held together by the peptide bonds between amino acids.

Question 15

The four structural levels of a protein are held together by different kinds of bonds. Explain the bonds that hold the Secondary Structure together.

Answer 15

_Secondary Structure _- held together by hydrogen bonds that form between nearby amino acids. These bonds create **α-helix chains **or β-pleated sheets.

Question 16

What are Hydrogen bonds?

Answer 16

Hydrogen bonds are weak bonds between a positive hydrogen atom in one molecule and a negative atom or group in another molecule.

Question 17

The four structural levels of a protein are held together by different kinds of bonds. Explain the bonds that hold the Tertiary Structure together.

Answer 17

_Tertiary structure _- this is affected by a few different kinds of bonds:

• Ionic interactions. These are **weak attractions **between **negative **and **positive **charges on different parts of the molecule.
• **Disulfide bonds/bridges. **Whenever two molecules of the amino acid **cysteine **come close together, the **sulfur **atom in one cysteine bonds to the sulfur atom in the other cysteine, forming a disulfide bond.
• **Hydrophobic **and hydrophilic interactions. When **hydrophobic **(water-repeling) groups are close togehter in the protein, they tend to clump together. This means that **hydrophilic **(water-attracting) groups are more likely to be pushed to the outside, which affects how the protein **folds up **into its final structure.
• Hydrogen bonds. These are weak bonds between a positive hydrogen atom in one molecule and a negative atom or group in another molecule.

Question 18

The four structural levels of a protein are held together by different kinds of bonds. Explain the bonds that hold the Quaternary Structure together.

Answer 18

_Quaternary structure _- this tends to be determined by the **tertiary structure **of the individual polypeptide chains being bonded together. Because of this, it can be influenced by **all the bonds **mentioned before:

• Peptide bonds
• Hydrogen bonds
• Ionic interactions
• Disulfide bonds/bridges
• Hydrophobic and hydrophilic interactions

Question 19

Protein shape relates to its function. Explain how the structure (protein shape) of **Collagen **relates to its function.

Answer 19

1. Collagen** **is a **fibrous protein **that forms **supportive **tissuses in animals, so it needs to be strong.
2. It’s made of **three polypeptide chains **that are **tightly coiled **into a strong triple helix.
3. The chains are interlinked by strong covalent bonds.
4. Minerals can bind to the triple helix to increase its rigidty.

Question 20

Protein shape relates to its function. Explain how the structure (protein shape) of Haemoglobin relates to its function.

Answer 20

1. **Haemoglobin **is a **globular protein **with an iron-containing **haem group **that binds to oxygen, **carrying it **around the body.
2. Its structure is curled up so that **hydrophilic **(water-attracting) side chains are on the **outside **of the molecule and **hydrophobic **(water-repelling) side chains face inwards.
3. This makes haemoglobin **soluble **in water, which makes it good for transport in the blood.