Structure and Function of proteins

Question 1

Proteins are functional products of the genome providing: (5)

Answer 1

1. Trafficking function - carrying oxygen around the body
   2, Metabolic functions - enzyme using and producing energy.
2. They make up cellular machinery - such as spliceosomes and nucleosomes.
3. Making up structural scaffolding - microtubules and nucleosomes.
4. Sensing molecules - receptors and their ligands

Question 2

Describe the structure of an amino acid (3)

Answer 2

The building blocks of proteins are amino acids. The basic structure of an amino acid is a tetrahedral arrangement of atoms around a central alpha carbon, linked to the C-alpha carbon are a carboxyl and amino group, a single hydrogen and a variable side chain usually represented by R.

Each protein’s 3D shape or conformation is key to its correct function and role in the cell.

Amino acids can occur in L- and D-forms, but only L-forms are used by cells.
Every amino acid (except glycine) can occur in two isomeric forms, because of the possibility of forming two different enantiomers (stereoisomers) around the central carbon atom. By convention, these are called L- and D- forms, analogous to left-handed and right-handed configurations. Only L-amino acids are manufactured in cells and incorporated into proteins. Some D-amino acids are found in the cell walls of bacteria, but not in bacterial proteins. e.g. Alanine

Question 3

What happens when the pH changes?

Answer 3

1. Each amino acid can exist in several different forms, depending on the pH of the environment. Amino acids tend to exist as “zwitterions” at an intermediate pH/ neutral (isoelectric point). When an amino acid is a zwitterion, the carboxyl group is deprotonated and negatively charged, while the amine group is protonated and positively charged.
2. At a low pH, then the carboxyl group gets protonated as well as the amine group being already protonated, this gives the amino acid a positive charge.
3. At a high pH then the amine group will get deprotonated (and no longer be ionised) and the carboxyl group will remain deprotonated. The overall charge is negative.
4. The “R” group on the amino acid may also possess a group that can be charged.

Question 4

Describe amino acid side chains (5)

Answer 4

1. There are twenty different side chains that may be grouped in various ways e.g. as polar/apolar or hydrophilic/ hydrophobic.
2. Ones that are polar are when the side chains tend to exist in the hydrophilic regions of the cell (these can be sub-divided into polar acidic, polar basic and polar neutral).
3. Non-polar amino acid side chains will tend to exist in the hydrophobic parts of the cell, they can be broken down into aliphatic (straight/branched chains) or aromatic (ring).
4. These can be further broken down into being acidic or basic.
5. Essential amino acids (of which there are 9) amino acids that our body cannot make, so we have to consume them in our diet.

Question 5

Formation of a polypeptide (2)

Answer 5

1. A polypeptide is a chain of amino acids, a protein could be constructed from several chains of polypeptides.
2. The defining feature of a polypeptide is the presence of the peptide bond which is formed by condensation reaction (water released) between the carboxyl and amino group on two different amino acids. There is a keto group from the carboxyl group and free H group from the amino group which are able to hydrogen bond, which is important in determining the structure of the protein/polypeptide.

Question 6

Describe the Primary, Secondary, Tertiary and Quartnery structure

Answer 6

On sheet (very long)

Question 7

Describe the relationship between haemoglobin and myoglobin (3)

Answer 7

1. An example of a protein in tertiary structure is myoglobin (found in muscle), whereas a protein in quaternary structure is haemoglobin.
2. The myoglobin consists of multiple alpha helices which bond to a haem group, the helices (tertiary structure) on the myoglobin are very similar to the tertiary structures of the alpha/beta chains in haemoglobin, despite having very different primary sequences. This gives them different binding affinities (myoglobin has a higher affinity). The haemoglobin chains can also undergo a conformational change to give them a higher/lower affinity depending on if in the lungs or muscle respectively.
3. Foetal haemoglobin also has a different affinity due to having a different primary structure, despite having a similar tertiary structure.

Question 8

Define Cofactor

Answer 8

A non-protein component necessary for the effective functioning of an enzyme.

Examples: Mg2+/ Zn2+
Haem in haemoglobin
NAD

Question 9

Define Coenzyme

Answer 9

Small organic non-organic protein molecules that bind temporarily to the active site of an enzyme molecule, either just or before an enzyme binds

e.g FAD

Question 10

Describe the shape and structure of a protein

Answer 10

1. Different proteins vary in size and shape. It may be determined in various ways, principally X-ray crystallography, and NMR. In proteins found in aqueous environments, the hydrophilic amino acid side chains are on the outside, the core of the protein will contain the hydrophobic residues.
2. Globular protein – spherical, water-soluble proteins e.g insulin
3. Conjugated protein - A globular protein with a prosthetic group (non-protein component). e.g. hemoglobin and catalase. E.g Haemoglobin

Question 11

Describe the structure of Haemoglobin? (4)

Answer 11

Sequence of amino acids joined by peptide bonds

Alpha helix, beta pleated sheets/turns and hydrogen bonds

2ndary structure/helix/polypeptide chain undergoes further coiling. 3 bonds form ionic/hydrogen/disulfide. Hydrophilic R-groups on outside of molecule/ hydrophobic on the inside.

4 polypeptides, 2 α and 2 β chains, 1 haem group per polypeptide. Prosthetic group – Fe2+