JESS'S A LEVELS: Biology: Chapter 2: Biological molecules: Proteins

Biology: Chapter 2: Biologica molecules: Proteins

Hydroxyl group

Carboxyl group

Amino group

Sulfhydryl

Methyl

Methyl group

Proteins are an extremely important class of macromolecules.
Proteins make up 50% of the dry mass of most cells.
Some of the many functions of proteins are as hormones, enzymes, antibodies, oxygen carrying pigments

Structure: Central carbon atom bonded to an amine group and a carboxylic acid group (-COOH-) and a Hydrogen.

The R group is what makes every amino acid different.
20 amino acids with different R groups occur naturally in proteins of living organisms
Many new ones have been synthesized in laboratories

Covalent bond between two amino acids
One amino acid loses a hydroxyl group (-OH-) from its carboxylic acid group (-COOH-)
The other loses a hydrogen from its amine group (-NHH-)
Carbon of 1st amino acid bonds with nitrogen from amine group of the 2nd.
Condensation reaction - H20 is removed
Dipeptide - Two amino acids bonded by a peptide bond
Polypeptide - Many amino acids linked by a peptide bond

Ribosomes - Site where amino acids join together to form polypeptides - controlled by enzymes
Peptide bond can be broken by adding H20 - hydrolysis - digestion of protein in stomach and small intestine

Structure of a protein molecule due to regular coiling/folding of the polypeptide chain of amino acids eg. alpha helices or beta pleated sheets
Amino acids in a polypeptide chain have an effect on each other even if they are not directly next to each other
Oxygen from -CO- group of one amino acid bonds to hydrogen of -NH- group of the amino acid four places ahead of it.

Easily broken by high temperatures and pH changes
Some proteins/ parts of proteins have no regular arrangement - depends on R groups of amino acids present therefore what attractions occur

Compact structure of 3D coiling of the already-folded chain(secondary structure) of the amino acids.
The secondary structure (folding) of the amino acid chain (alpha helix or beta pleated sheet) coiled into a 3-dimensional (3D) structure
Although it may look random and disorganized, the shape is very precise for each protein and is held in shape by four different types of bonds between amino acids in the chain.

Disulfide bonds - Strong double covalent bond formed between the sulfurs of two cysteine molecules (S=S)
Ionic bonds - Bond between two oppositely charged R groups (NH3+ and COO- groups). Can be broken by pH changes.
Hydrogen bonds - Between strong polar groups eg. -NH-, -CO- and -OH- groups
Weak hydrophobic interactions - Between non polar R groups. Hydrophobic R groups are repelled by the watery environment around them and stick together, though these bonds are weak.

The tertiary structure of a protein can be broken by heat - increasing the kinetic energy makes the molecules vibrate more, so bonds holding the structure in shape (which are mostly weak non-covalent bonds) are more likely to break, and therefore changing its shape. This is called denaturing.

3D arrangement of two or more polypeptide chains or a polypeptide chain and a non protein molecule
Forms a protein
Bonded by the same four bonds used in the tertiary structure

Proteins whose molecules curl up into a 'ball' shape.
Usually curl up so that the non-polar, hydrophobic R groups point towards the centre of the molecule, away from the watery environment.
Most globular proteins are soluble - hydrophilic R groups on the outside of the protein, therefore water molecules cluster around them.
Enzymes are globular proteins

Oxygen carrying pigment in red blood cells
Globular protein
Made of four polypeptide chains - quaternary structure
Each chain is known as a globin
Two of the haemoglobin chains are called alpha chains and made from alpha-globin, while the two other ones are made from beta chains and are called beta-globin.
The hydrophobic R groups point inside while the hydrophilic R groups are on the outside.
Hydrophilic R groups on the outside maintain the haemoglobin's solubility.
Interactions between hydrophobic R group on the inside help maintain it's correct 3D shape.
Sickle cell anemia: Glutamic (hydrophilic amino acid) on the surface beta-chain is replaced with Valine (hydrophobic amino acid) - non-polar R group on the outside makes it less soluble.
Prosthetic group: Important part of a protein molecule not made of amino acids
Each polypeptide chain has a prosthetic haem group
Each haem group has an iron atom, which can bind with O2 (two oxygen atoms).
Therefore a complete haemoglobin molecule can bind with 4 oxygen molecules (8 oxygen atoms) at one time since there are four polypeptide chains.
Haem group is responsible for colour of haemoglobin, depending on whether iron atoms have combined with oxygen.
Oxyhaemoglobin - When the iron atoms are combined with oxygen.

Fibrous protein
Makes up 25% of total protein in mammals - most common
Structural protein
Consists of 3 polypeptide chains wound around each other in the shape of a helix (triple helix)
Almost every third amino acid is glycine, the smallest amino acid - found on the inside, allows 3 strands to lie closer together and form a tight coil, since any other amino acid would be too large.
Fibrils: Each 3 stranded collagen molecule interacts with other collagen molecules parallel to it. Covalent bonds form between R groups of amino acids next to each others, forming cross-links which hold many collagen molecules side by side forming the fibrils.
Fibres: Strong bundle of many fibrils lying alongside each other.
Collagen fibres line up according to forces they must withstand.
Flexible but can withstand large tensile strength - withstand large pulling forces without stretching or breaking.
Achilles tendon can withstand a pulling force of 300N