2.2 Proteins

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  • Created by: Emily
  • Created on: 05-12-17 10:01

Functions of Proteins

  • Important biological molecule - comprises 50% of dry mass.
  • Forms structural components of animals e.g. muscle contains actin & myosin.
  • Tendency to adopt specific shapes --> proteins are important as enzymes, antibodies & some hormones.
  • Membranes:
    • Protein lined channels for transport of ions and polar molecules.
    • Carrier proteins are involved in active transport and facilitated diffusion.
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How Are Proteins Made?

  • Proteins are large polymers comprised of long chains of amino acids.
  • Both plants and animals need amino acids to make proteins.
  • Animals can make some amino acids, but must ingest essential amino acids.
  • Plants can make all the amino acids they need if they can access fixed nitrogen.
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Structure of Amino Acids

  • Amino acids are the building blocks from which protein is made.
  • Only 20 out of over 500 amino acids are proteinogenic (found in proteins).
  • Amino acids have a central carbon atom surrounded by:
    • a carboxyl (-COOH) group
    • an amino (NH2) group
    • a hydrogen
    • a variable R group
  • They are joined together by covalent bonds called peptide bonds.
  • Making a peptide bond involves a condensation reaction.
  • Breaking a peptide bond involves a hydrolysis reaction.
  • Protease enzymes in the intestine break peptide bonds during digestion.
  • Two amino acids joined together are known as a dipeptide.
  • Joining a long chain of amino acids together forms a polypeptide.
  • A protein can consist of one or more poplypeptide chains bonded together.
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Primary Structure

  • The sequence of amino acids in a protein chain.
  • The function of a protein is determined by its structure.
  • Changing just one amino acid alters the function of the protein.
  • Held together by peptide bonds = covalent bonds = very strong.
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Secondary Structure

  • The coiling or folding of an amino acid chain, which arises often as a result of hydrogen cond formation between different parts of the chain.

Alpha Helix:

  • 36 amino acids per 10 turns of the helix.
  • 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.

Beta-pleated sheet:

  • An amino acid chain folds over on itself.
  • Hydrogen bonds between the -NH group of one amino acids and the -CO group of another further down the chain hold it together.

Hydrogen Bonds:

  • They are relatively weak but provide stable structures when many are formed at optimal temperature and pH.
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Tertiary Structure

  • The overall 3D shape of a protein molecule.
  • Formed when coils and pleats start to fold along with areas of straight chains of amino acids.
  • Very precise shape held firmly in place by bonds between amino acids.
  • Supercoil shape in fibrous proteins.
  • Spherical shape in globular proteins.
  • Held together by hydrogen bonds, ionic bonds, disulfide links and hydrophobic & hydrophilic interactions.
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Quaternary Structure

  • Multiple polypeptide chains are held together are arranged to make the complete protein molecule.
  • Held together by hydrogen bonds, ionic bonds, disulfide links and hydrophobic & hydrophilic interactions.
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Protein Bonding

Hydrogen bonds:

  • Form between H atoms with a slightly + charge and other atoms with a slight - charge.
  • In amino acids, these form in hydroxyl, carboxyl and amino groups.
  • Keep 3o and 4o structure in shape and provide strength when multiple bonds are present.

Ionic bonds:

  • Form between the NH3+ and COO- of R groups, but easily broken by pH changes.

Disulfide links:

  • Formed between R groups of two cysteines.
  • Strong covalent bonds, but are broken by reducing agents.

Hydrophobic and hydrophilic interactions:

  • Hydrophobic parts of the R group associate in the centre of the polypeptide.
  • Hydrophilic parts are founds at the edge of the polypeptide to be close to water.
  • These interactions cause the twisting of the chain, changing the shape of the protein.
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Fibrous Proteins

  • Have regular, repetitive sequences of amino acids with a long, thin structure.
  • Usually insoluble in water as they have a high proportion of amino acids with hydrophobic R groups.
  • Form fibres or filaments which have a structural function.
  • Have a supercoiled helix shape.
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Fibrous Proteins: Collagen

  • Function = provide mechanical strength.
  • In artery walls, a layer of collagen prevents the artery from bursting when withstanding high pressure from blood being pumped by the heart.
  • Form tendons, connecting muscles to bones, allowing them to pull on bones.
  • Form bones & reinforced with calcium phosphate.
  • Form cartilage and connective tissue.
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Fibrous Proteins: Keratin

  • It is rich in cysteine so lots of disulfide bridges form between polypeptide chains, making the molecule very strong.
  • It is found wherever a body part needs to be strong, including:
    • Finger nails
    • Claws
    • Hooves
    • Scales
    • Fur
    • Feathers
  • Provides mechanical protection
  • Provides and impermeable barrier to infection
  • Is waterproof so prevents entry of water-borne pollutants
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Fibrous Proteins: Elastin

  • Cross linking and coiling make the structure of elastin strong and extensible.
  • Found in living things which need to stretch and adapt their shape as part of life processes.
  • Elastin causes skin to stretch around our bones and muscles, and returns it to its normal shape.
  • Elastin in the lungs allows them to inflate and deflate.
  • In the bladder elastin allows it to expand to hold urine.
  • It helps blood vessels to stretch and recoil as blood is pumped through them, helping to miantain the pressxure wave of blood as it passes through.
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Globular Proteins

  • Tend to roll up into a spherical shape.
  • Any hydrophobic R groups are turned inwards towards the centre of the molecule, while hydrophilic groups are on the outside, which makes the protein water soluble because water molecules can easily cluster round and bind to them.
  • They often have very specific shapes, helping them to take up metabolic roles as enzymes, hormones and haemoglobin.
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Globular Proteins: Haemoglobin

  • The quaternary structure of haemoglobin conists of two alpha-globin chains and two beta-globin chains, which fit together to form a haemoglobin molecule.
  • Each chain has a haem group, which is called a prosthetic group because it is an essential part of the molecule but it is not made of amino acids.
  • A protein associated with a prosthetic group is called a conjugated protein.
  • The haem group contains an iron ion.
  • The function of haemoglobin is to carry oxygen from the lungs to the tissues. It does this by:
    • In the lungs an oxygen molecule binds to the iron in each of the four haem groups.
    • Binding turns haemoglobin from purple red to bright red.
    • Oxygen is released by haemoglobin when it reaches the tissues.
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Globular Proteins: Insulin

  • Made of two polypeptide chains:
    • The A chain begins with a section of alpha-helix.
    • The B chain ends eith a section of beta-pleat.
    • Both chains fold into a tertiary structure and are joined together by disulfide links.
  • Soluble in water.
  • Insulin binds to glycoprotein receptors on the outside of muscle and fat cells to:
    • Increase uptake of glucose from the blood.
    • Increase their rate of consumption of glucose.
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Globular Proteins: Pepsin

  • Pepsin is an enzyme that digests protein in the stomach.
  • It is made up of a single polypeptide chain of 327 amino acids, but folds into a symmetrical tertiary structure.
  • It only has 4 amino acids with basic R groups, but 43 with acidic R groups.
  • This means that it is very stable in the acidic environment of the stomach, as there are few basic groups to accept H+ ions, which has little effect on the enzyme's structure.
  • The tertiary structure is also held together by hydrogen bonds and two disulfide bridges.
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Computer Modelling of Protein Structure

  • Predicting the shape of a protein molecule can be very useful in biochemistry e.g. helping to identify new medicines.
  • Techniques for the prediction of secondary structure were based on the probability of an amino acid being in a particular secondary structure. This information was derived from already-known protein molecular structures.
  • Tertiary structure can be predicted using two approaches:
    • Ab initio protein modelling is when a model is built based on the physical and electrical properties of the atoms of each amino acid in the sequence. However, there can be multiple solutions so other methods can be required to eliminate the number of options.
    • Comparitive protein modelling - one approach is protein threading, which scans the aminos acid sequence against a database of solved structures and produces a set of models to match the sequence.
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