2.2.8(Proteins)

Define the term amino acid

• Monomers of all proteins with the same basic structure

Describe the role of proteins

• They are structural components of animals

• They adopt specific shapes which makes them important as enzymes, antibodies and some hormones

• Membranes have proteins that act as carriers ad pores for active transport and facilitated diffusion

State the elements which make up an amino acid

• carbon

• hydrogen

• oxygen

• Nitrogen

• some contain sulfur

State the functional groups of amino acids and draw the standard amino acid structure

• Amino group(-NH2)

• Carboxyl group(-COOH)

State the name of the bond which holds amino acids together

• Peptide bonds

State the enzyme which helps to catalyse the break down of proteins

• Protease - by breaking peptide bonds

What is the peptide bond structure

• C double bond O, N H

What is meant by the primary structure of a protein

• The sequence of amino acids in a protein chain is its primary structure

What is meant by the secondary structure

• The coiling or folding of an a primary structure, due to hydrogen bonding between different parts of the polypeptide chain

What are the 2 main Secondary structures?

• alpha helix sturcture

• beta pleated sheet

Describe the structure of an alpha helix structure

• Helix structure which is spiraled

• The helix is held together by lots of hydrogen bonds between the -NH group of one amino acid and the -C=O of another amino acid, 4 places ahead of it in the chain

Describe the structure of a beta pleated sheet structure

• It has a zigzag structure which is folded in on itself

• Hydrogen bonds form between the -NH of one amino acid and the C=O of another amino acid further down the strand which holds the sheet together

Explain why secondary structures are stable.

• Although hydrogen bonds are weak, many of them are formed between -NH and -C=O groups which makes the entire structure strong and stable at optimal temperatures and pH

What meant by a tertiary structure

• It is the overall 3D shape of a protein molecule, that arises due to hydrogen bonding, disulphide bond, ionic bonds and hydrophilic and hydrophobic interactions

Describe how hydrogen bonds are formed between amino acids in polypeptide chains

• They form between a slightly positive hydrogen and a slightly negative oxygen, in amino acids, these form between hydroxyl, carboxyl and amino groups

State the importance of hydrogen bonding in proteins

• Hydrogen bonds are important in keeping the tertiary and quaternary structure of the protein in the correct shape.

• The presence of multiple hydrogen bonds can give protein molecules a lot strength

Describe how ionic bonds form

• They form between carboxyl and amino groups that are part of R groups

• These ionise into NH3+ and COO- groups

• Positive and negative groups like thus are strongly attracted to each other to form ionic bonds

Describe how disulfide links form

• The R group of the amino acid cysteine contains sulfur. Disulfide bridges are formed between the R groups of 2 cysteines

• These are strong covalent bonds

Describe how hydrophobic and hydrophilic interactions take place in proteins?

• Hydrophobic parts of the R groups tend to associate together in the centre of the polypeptide to avoid water. In the same hydrophilic parts are found at the edge of the polypeptide, close to water

• Hydrophilic and hydrophobic interactions cause the twisting of the amino acid chain, which changes the shape of the protein

Explain why hydrophilic and hydrophobic interactions are important

• The hydrophilic and hydrophobic interactions are important as most proteins are found surrounded by water inside a living organism

What are the 2 main categories of tertiary and quaternary structured proteins

• Globular

• Fibrous

State structure and function of fibrous proteins

• They have a regular, repetitive sequences of amino acids

• Usually insoluble in water

  • These features enable them to form fibres which tend to have a structural function

State the structure and function of Globular proteins

• They roll up into an almost spherical shape.

• Any hydrophobic R-groups are turned inwards towards the centre of the molecule, while hydrophilic groups are on the outside.

  • This makes the proteins soluble in water

• They often have very specific shapes, which help them to take up specific roles

Compare Globular and fibrous proteins

• Fibrous:

  • Shape: Long, Narrow

  • Role: Structural(strength)

  • Solubility: generally insoluble in water

  • Sequence: Repetitive amino acid sequences

  • Stability: Less sensitive to changes in Heat, pH, etc.

  • Examples: Collagen, Keratin, Elastin, Myosin

• Globular:

  • Shape: Rounded

  • Role: Functional(catalytic, transport etc.)

  • Solubility: Generally soluble in water

  • Sequence: Irregular amino acid sequence

  • Stability: More sensitive to changes in temperature, pH

  • Examples: Haemoglobin, Insulin, Pepsin

State the function of collagen as a fibrous protein and 4 examples of their function being used.

• Function: Provide mechanical strength:

• Examples:

  • Artery walls: Collagen prevents bursting and withstands high pressure

  • Tendons: made of collagen and connect muscle to bone

  • Bones: Made of collagen and reinforced with calcium phosphate - making them hard

  • Cartilage and connective tissue: Made from collagen

State the function of cross links in collagen

• They are staggered to avoid weak points

State the structure and function of keratin

• Function:

  • Provide mechanical protection

  • Impermeable barrier to infection which prevents entry of water-born pollutants

• Structure:

  • Rich in cysteine, causing lots of disulfide bridges from between its polypeptide chains.

  • Along side hydrogen bonds makes the molecule very strong

State where keratin is found in the body

• It is found in body parts that need to be hard and strong:

  • Fingernails

  • Hair

  • Claws

  • Hoofs

  • Horns

  • Scales

  • Fur

  • Feathers

State the structure and function of elastin

• Structure: Crosslinks and coiling make the structure of elastin strong and extensible.

• Function: To provide stretch and adapt shape as part of their processes

State 3 ways in which elastin is used in the body

• Skin: Skin can stretch around our bones and muscles because of elastin which allows skin to go back to normal after being pinched

• Lungs and bladder: It is found in out lungs to allow them to inflate and deflate and in out bladder, which helps it expand to hold urine

• Blood vessels: Elastin helps out blood vessels stretch and recoil, helping maintain pressure of blood

State what collagen, keratin and elastin are examples of

• Fibrous proteins

State the structure and function of haemoglobin

• Structure: (Quaternary structure)

  • Made up of 4 polypeptide chains:

    • 2 alpha-globin chains and 2 beta-globin chain

    • Each of these has its own tertiary structure, but when fitted together they form one haemoglobin molecule

  • The shape of the molecule is held together by hydrogen bonds, hydrophobic and hydrophilic interactions and ionic bonds which gives it a very specific shape

  • Each polypeptide subunit has a haem group which are called prosthetic groups

  • Haemoglobin is a conjugated, globular protein

  • When oxygen binds, haemoglobin turns from a purple red colour to bright red

• Function:

  • To carry oxygen from lungs to respiring tissue. It does this by binding to the iron group in each haem group

State the structure and function of insulin

• Structure:

  • Made of 2 polypeptide chains:

    • The A chain begins with a section of alpha helix, and the B chain ends with a section of Beta pleat.

    • Both chains fold into a tertiary structure and are then joined by disulfide links

    • Amino Acids with hydrophilic R groups are on the outside of the molecule, which makes it soluble in water

• Function:

  • Binds to glycoprotein receptors on the outside of the muscle and fat cells to increase their uptake of glucose from the blood and to increase their rate of consumption

State the strucure and function of pepsin

• Structure:

  • Made up of a single polypeptide chain of 327 acids, but it folds into a symmetrical tertiary structure.

  • Pepsin has a few amino acids with only 4 basic R groups

  • Pepsin has 43 amino acids with acidic R groups

    • there are few basic groups that accept H+ ions and therefore can be little effect on the enzyme’s structure which explains it’s stability in acidic environments

• Functions:

  • An enzyme which digests proteins in the stomach

State and explain 2 ways in which structures of proteins can be predicted

• Ab initio protein modelling:

  • A model built based on the physical and electrical properties of atoms in each amino acid in the sequence. There can multiple solutions to the same amino acid sequence and other methods sometimes need applying to reducing the number of solutions

• Comparative protein modelling:

  • Protein threading is one approach, which scans the amino acid sequence against a data base of known structures and produced a possible set of models which would match that sequence