Week 1 (protein)

Question 1

Name the three parts making up an amino acid

Answer 1

Carboxyl group
Amino group
Side chain (R group)

Question 2

How do you classify amino acids?

Answer 2

By their R groups

Question 3

Name the classifications of amino acids R groups

Answer 3

Aromatic R groups
Positively charged R groups
Polar uncharged R groups
Nonpolar aliphatic R groups
Negatively charged R groups

Question 4

How are amino acids linked in a polypeptide chain?

Answer 4

They are linked covalently by a peptide bind.

Question 5

How does a peptide bond form?

Answer 5

It is formed via a condensation reaction between the amino group of one amino acid and the hydroxyl group of another.
A water molecule is released.

Question 6

Name the chains of amino acids form in order of size/complexity

Answer 6

Dipeptides/tripeptides
Oligopeptides
Polypeptides
Proteins

Question 7

In what order are amino acid sequences written in?

Answer 7

Written from the first amino group to the last carboxyl group.

Question 8

Define oligomeric

Answer 8

If at least two polypeptide chains in the protein are identical

Question 9

Define protomers

Answer 9

An identical unit in a protein

Question 10

What do simple proteins contain?

Answer 10

Only amino acids

Question 11

What doe conjugated proteins contain?

Answer 11

Additional permanently associated chemical components.

Question 12

What is a prosthetic group?

Answer 12

The non-amino acid part of a protein.
Some proteins have more than one prosthetic group.

Question 13

How do we classify conjugated proteins?

Answer 13

On the basis of their prosthetic group

Question 14

Describe the primary protein structure

Answer 14

Sequence of a chain of amino acids

Question 15

Describe the secondary protein structure

Answer 15

Local folding of the polypeptide chain into helices or sheets

Question 16

Describe the tertiary protein structure

Answer 16

3D folding pattern of a protein due to side chain interactions

Question 17

Describe the quaternary protein structure

Answer 17

Protein consisting of more than one amino acid chain.

Question 18

Describe the structure of an alpha helix (secondary structure)

Answer 18

Amino acids and carboxyl groups of amino acids go into the middle of the helix whilst the R groups stick out.

Question 19

Describe the hydrogen bonding that occurs in an alpha helix

Answer 19

Hydrogen bonds occur every three residues.
They continue all the way up the alpha helix and will occur inside the helix.
The binding that occurs gives the protein its secondary structure.

Question 20

What does delta delta G angle show?

Answer 20

How likely it is going to form an appropriate hydrogen bond and help with the formation of an alpha helix.
The higher the number the more difficult it will be take up the alpha helical structure.

Question 21

Describe the structure of beta strands and beta sheets (secondary structure)

Answer 21

zigzag or ‘pleated’ structure
Several beta-strands can pack together to form a beta-sheet.

Question 22

Describe the hydrogen bonding between the beta sheets/strands

Answer 22

Bonding occurs between the beta strands to create a beta street.

Question 23

Why is hydrogen bonding between strands stronger in antiparallel beta sheets?

Answer 23

The C=O and N-H groups are better aligned.

Question 24

What does circular dichroism identify?

Answer 24

Secondary structures of a protein

Question 25

How does circular dichroism work?

Answer 25

Circularly polarised UV light is absorbed differently by alpha-helices, beta-sheets and unstructured regions of proteins.

Question 26

Name and describe the 5 bond types in tertiary structure

Answer 26

Hydrophobic interactions: these amino acids orient themselves towards the centre of the polypeptide to avoid the water.
Disulphide bridge: the amino acid cysteine forms a bond with another cysteine through its R group.
Hydrogen bonds: polar ‘R’ groups on the amino acids form bonds with other polar R group.
Hydrophilic interactions: these amino acids orient themselves outward to be close to the water.
Ionic bonds: positively charged R groups bond together.

Question 27

Describe fibrous proteins

Answer 27

• long sheets
• extensive regions of a single type of secondary structure
• insoluble (rich in hydrophobic residues)
• most proteins that provide support, shape, and external protection to vertebrates.

Question 28

Describe globular proteins

Answer 28

• roughly spherical shape
• often soluble (hydrophobic residues burrow inside, hydrophilic residues stick outside
• most enzymes and regulatory proteins

Question 29

What can the accumulation of misfolded proteins lead to?

Answer 29

Alzheimer’s
Parkinson’s

Question 30

Name the 4 common ways to denature proteins

Answer 30

Heat: breaks weak interaction, including hydrogen bonds.
Change pH: disrupts electrostatic interactions
Detergents: disrupts hydrophobic effect
Chaotropic agents: disrupts hydrogen bonds and hydrophobic effect.

Question 31

What is a ligand?

Answer 31

A molecule that reversibly binds to a protein.
Proteins are specific for their ligands.

Question 32

Where do ligands bind to proteins?

Answer 32

At its binding site (complements the ligand’s size, shape and charge)

Question 33

Describe the process of ligand association and ligand disassociation

Answer 33

Association: when a protein binds a ligand
Disassociation: when the ligand is released

Question 34

What is Kd?

Answer 34

Disassociation constant

Question 35

What does Kd measure?

Answer 35

The level of affinity.
A protein that binds a ligand very tightly will have a low Kd so have high affinity. A lower concentration of ligand is needed to occupy half of the binding sites.

Question 36

Describe the structure of haemoglobin

Answer 36

A red protein which is responsible for transporting oxygen in the blood of vertebrae.
Composed of four polypeptide chains.
A tetramer composed of two alpha and two beta subunits.
Binds with 4 oxygen molecules.
Exhibits cooperative binding with oxygen.
Has a low affinity to bind with oxygen.
Takes oxygen from lungs and transports to the rest of the body.

Question 37

Describe the structure of myoglobin

Answer 37

A red protein with haem which carries and stores oxygen in the muscle cells.
Composed of a single polypeptide chain.
A monomer and lacks quaternary structure.
Binds with a single oxygen molecule.
Does not exhibit cooperative binding with oxygen.
Has a high affinity to bind with oxygen (does not depend in the oxygen concentration).
Stores oxygen in the muscle cells and releases it when needed.

Question 38

How does haemoglobin bind and release to oxygen?

Answer 38

Binding: Hb binds to oxygen in the lungs where partial pressure of oxygen is high.
Release: Hb releases oxygen in tissues where the partial pressure of oxygen is lower.

Question 39

How does haemoglobin bind and release to carbon dioixide?

Answer 39

Binding: carbon dioxide directly binds to amino acid residues on the haemoglobin molecule.
Release: Carbon dioxide is release from Hb in the lungs where the partial pressure of carbon dioxide is lower.

Question 40

How does haemoglobin bind and release to hydrogen?

Answer 40

Binding: Hb binds to hydrogen ions which are released during the conversion of carbon dioxide to bicarbonate ions.
Release: hydrogen ions are released when Hb binds with oxygen.