Proteins

Question 1

what is proteins

Answer 1

Proteins are large polymers composed of amino acid chains.

Question 2

protein functions:

Answer 2

•Structural components of animals, for example muscles.
•Tendency to adopt specific shapes makes proteins important as enzymes, antibodies and hormones.
•Carriers and pores for active transport/facilitated diffusion across a membrane.

Both plants and animals need amino acids to make proteins, animals must ingest essential amino acids to make them, plants make them if they have access to fixed nitrogen (e.g. nitrates).

Question 3

Amino Acids:

Answer 3

•All contain N, O and H, some contain S in the R group.
Amino acids have an amino (-NH2) group, carboxyl (-COOH) group and R-group. Radical groups are different in each amino acid (glycine has just an H atom, whereas cysteine has CH3S). R groups vary in size and polarity with some being hydrophobic and some hydrophilic.

•When dissolved in water the amino group and carboxyl group ionise, the amino group accepts an H+ ion and becomes NH3+, and the carboxyl group loses an H+ from the OH and becomes COO-.

•Amino acids can act as buffers, at low pH (i.e. lots on H+ ions), they will accept H+ ions, in high pH they release them. This means they have both acidic and basic properties (amphoteric). Protein chains are affected by the amphoteric nature of amino acids, by accepting/releasing H+ ions, amino acid can help regulate pH changes – this is known as buffering (a buffer is a substance that helps resist large pH changes).

Question 4

Peptide bonds:

Answer 4

Covalent bonds between the N of an amino group and the C of a carboxyl group, that joins amino acids. Formation of a peptide bond (like glycosidic and ester) involves a condensation reaction and breaking involves hydrolysis. Protease enzymes in digestion catalyse this hydrolysis reaction.

All amino acids join in the same way, independent of their different R groups. Two amino acids – dipeptide, multiple - polypeptide. Proteins consist of a polypeptide chain or multiple ones bonded together.

Question 5

Protein structures

Answer 5

Primary
Secondary
Tertiary
Quaternary

Question 6

Primary structure:

Answer 6

The sequence of amino acids in a molecule. The number and order of amino acids is important. The function of a protein is determined by its structure, there are 20 possible amino acids, so lots of combinations in a 100-long chain. Changing 1 amino acid may change the structure of the whole protein.

The primary structure is held together by peptide bonds.

Question 7

Secondary structure:

Answer 7

The coiling or folding of amino acid chains – due to hydrogen bonding between different parts of the chain.
• α-helix: Coils held together by hydrogen bonds between the -NH group of one amino acid and the - CO group of another four places ahead of it in the chain. Hydrogen bonds are within the chain.
• β-pleated sheet: Zig-zag structure held again by a -NH group hydrogen bonded to a -CO further down the strand. Hydrogen bonds between different sheets.
Although hydrogen bonds are relatively weak, many are formed which makes these two structures stable at optimum temp/pH. Some chains may have more than one secondary structure at different ends (insulin).

The secondary structure is primarily held together by hydrogen bonds.

Question 8

Tertiary structure:

Answer 8

The overall 3D shape of a protein molecule. Its shape arises due to interactions including hydrogen bonding, disulphide bridges, ionic bonds and hydrophobic/hydrophilic interactions. The tertiary structure may adopt a supercoiled shape – fibrous proteins, or a more spherial shape – globular proteins.

The tertiary and quaternary are held together by many – between polypeptide chains.

Question 9

Quaternary structure:

Answer 9

Protein structure where a protein consists of more than one polypeptide chain (e.g. insulin). It describes how multiple polypeptide chains are arranged to make the complete molecule. Same bonding as tertiary.

The tertiary and quaternary are held together by many – between polypeptide chains.

Question 10

Protein bonding

Answer 10

Ionic bonds
Disulfide bridge
Hydrophilic and hydrophobic intersections
Hydrogen bonds

Question 11

Ionic bonds:

Answer 11

When the carboxyl groups and amino groups ionise into NH3+ and COO-, the strong attraction between these positive and negative ions forms an ionic bond.

Question 12

Disulfide Bridges:

Answer 12

The R group of the amino acids cysteine contains sulphur. Disulfide bridges are formed between the R groups of two cysteines. They are strong covalent bonds.

Question 13

Hydrophobic and hydrophilic interactions:

Answer 13

Hydrophobic parts of the R groups tend to associate in the centre of the polypeptide to avoid water, hydrophilic parts are found on the edges. Hydrophobic and hydrophilic interactions cause the twisting on the amino acid chain, which changes the shape of the protein. These interactions have a big influence as most proteins are found surrounded by water in an organism.

Question 14

Hydrogen bonds:

Answer 14

Between Hydrogen atoms with a slight + charge and other atoms with a slight – charge. In amino acid these form in hydroxyl, amino and carboxyl groups. They may form between the carboxyl group of one amino acid and the amino group of another, or between polar regions of R groups. They keep the secondary, tertiary and quaternary structures in shape, many hydrogen bonds give a protein molecule lots of strength.

Question 15

Fibrous Proteins:

Answer 15

Relatively long, thin structure, insoluble in water and metabolically inactive, often having a structural role within an organism. Regular, repetitive sequences of amino acids – enabling them to form fibres. Formed from parallel polypeptide chains, held together by cross links.

•collagen
•keratin
•Elastin

Question 16

Collagen:

Answer 16

Function is to provide mechanical strength:

• Artery walls – a layer of collagen prevents bursting and allows it to withstand high pressure of blood pumped from the heart.
• Tendons – connect bones to muscles, allowing them to pull on bones.
• Bones – made from collagen, reinforced with calcium phosphate – hardness.
• Cartilage and connective tissue.

Question 17

Keratin:

Answer 17

Rich in cysteine so lots of disulfide bridges form between polypeptide chains. Alongside hydrogen bonding this makes it strong.
Found in: Fingernails, hair, claws, hoofs, horns, scales, fur and feathers. Provides mechanical protection and an impermeable barrier to infection, being waterproof, prevents entry of water born pollutants.

Question 18

Elastin:

Answer 18

Cross-linking and coiling, makes it strong and extensible. Found in living things that need to stretch or adapt their shape.
• Skin – stretching around bones and muscles, allows skin to return to normal shape after stretching.
• Lungs – inflating and deflating. Bladder – expanding to hold urine.
• Blood vessels – stretch and recoil as blood is pumped through them, helping to maintain pressure.

Question 19

Globular Proteins:

Answer 19

Haemoglobin
Insulin
Pepsin

Question 20

Globular proteins

Answer 20

Relatively spherical molecules, soluble in water, often have metabolic roles.
Tend to roll up into an almost spherical shape caused by highly folded polypeptide chains. Hydrophobic R groups turned inwards towards centre, with hydrophilic parts on the exterior – this makes the molecules soluble as water can bind to the exterior. They often have specific shapes, so they can take up roles as enzymes, hormones (e.g. insulin) and haemoglobin.

Question 21

Haemoglobin (transport protein):

Answer 21

The quaternary structure of haemoglobin is made up of 4 polypeptides: 2 a-globin chains and 2 B-globin chains. Each has its own tertiary structure but fit together to form one molecule. The interactions between the polypeptides give the molecule a specific shape. On each chain there is a space where a haem group is held - this is a prosthetic group.

Prosthetic group:
•A non-protein component that forms a permanent part of a tunctioning protein molecule
•conjugated protein: a protein with a prosthetic group

Function: Carry oxygen from lungs to tissues. In the lungs an O2 molecule binds to an Fe2+ ion in each of the haem groups, when it binds the haemoglobin turns a purple colour, from red. It is soluble.

Question 22

Insulin (hormone):

Answer 22

Made by pancreas, 2 polypeptide chains, with different secondary structures at different ends. Both chains fold into a tertiary structure, joined by disulfide links. Amino acids with hydrophilic R groups are on the
exterior of the molecule - soluble. Insulin binds to g vcoprotein receptors on the outside of muscle and fat cells to increase their uptake of glucose from blood, and to increase their consumption rate of glucose.

Question 23

Pepsin (enzyme):

Answer 23

Digests protein in the stomach, made up of 1 polypeptide chain (no quaternary structure), but it folds into a symmetrical tertiary structure (held together by 2 disulfide bridges and hydrogen bonding). Pepsin has few amino acids with basic R groups, but many with acidic R groups - therefore its optimum pH is approx. 2.
There are few basic groups to accept H* ions so they have little effect of the enzyme’s tertiary structure.