Proteins Part 2 Review of protein structure, Types of Proteins, Testing for Proteins

Where are amino acids linked? In living cell Ribosomes! These reactions that occur on the ribosomes are controlled by ENZYMES (more on this later)

How are polypeptides broken? Hydrolysis Reactions Naturally occurs in stomach and small intestine Protein in food is hydrolyzed into amino acids prior to being absorbed by the blood Once in the blood, these AA can be restructured into polypeptides and then twisted and folded into functioning PROTEINS the cells in you body needs

Protein Structure the association of the polypeptide chains Primary structure 1’ Order of amino acids in a polypeptide chain Secondary structure 2’ Polypeptide chain folds because of interactions between amino acids HYDROGEN BONDING Tertiary Structure 3’ Gives proteins 3-D shape VERY IMPORTANT to function of protein Beta pleated sheets and alpha helices fold based on interactions between R-groups of a.a. Hydrogen bonds, polar/non-polar interactions, acid/base interactions, disulfide bonds, van der Waals forces Quaternary Structure 4’ the association of the polypeptide chains some proteins contain more than one polypeptide chain Each polypeptide chain in the protein is called a subunit Two or more subunits come together for a specific function HEMOGLOBIN On Red blood cells Its shape allows RBCs to carry oxygen all around your body!

Primary Structure Sequence of AA in a long polypeptide chain AA= letters of alphabet Sequence of AA= arrangement of letters to make words HUGE amount of different primary structures Changing ONE AA is polypeptide chain GREATLY changes the properties of the polypeptide chain and PROTEIN

Secondary Structure Three possible 2o structures Determined by order R-groups No particular arrangement Alpha helix Polypeptide chains that coil tightly Beta pleated sheet Looser, straighter shape created by hydrogen bonds The order of AA in polypeptide chain determine interactions between functional groups of AA Functional groups interact via HYDROGEN BONDS Attraction between oxygen in the –CO end of one AA and the hydrogen in the – NH end of another AA H-bond easily broken Change pH and change Temperature

Tertiary Structure Secondary structure gets coiled and folded Precise 3D shape Folding is determined by interactions between R-groups Hydrogen bonds Tryptophan Arginine Asparigine Disulphide bonds Between 2 cystine molecules Ionic bonds b/t R groups containing amine and carboxyl groups Hydrophobic interactions b/t R groups that are non-polar (hydrophobic)

2 main types of tertiary structures Globular form ball-like structures where hydrophobic parts are towards the centre and hydrophilic are towards the edges Structure=water soluble Found in watery environments cells, tissue fluid, or in fluids being transported (blood or phloem) metabolic roles Ex: enzymes in all organisms, plasma proteins and antibodies in mammals Fibrous form long fibres mostly consist of repeated sequences of amino acids which are insoluble in water usually have structural roles Ex. Collagen in bone and cartilage Keratin in fingernails and hair

Quaternary Structure Proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (for example, a haem group in haemoglogin) Prosthetic Group (inorganic component of protein) These proteins will only be able to function if all subunits are present Made by same bonds found in tertiary structure Interactions between R-groups Hydrogen bonds Tryptophan Arginine Asparigine Disulphide bonds Between 2 cystine molecules Ionic bonds b/t R groups containing amine and carboxyl groups Hydrophobic interactions b/t R groups that are non-polar (hydrophobic)

Special Proteins Spherical 3D shape Ex. Haemoglobin, insulin, enzymes Globular Fibrous Spherical 3D shape Ex. Haemoglobin, insulin, enzymes Water soluble Physiologically active Metabolic and transport roles Do not curl up in 3D ball Long, thin molecules Molecules lie side-by-side to form fibres Insoluble in water Not physiologically active STRUCTURAL roles

Haemoglobin Water soluble globular protein Structure two α polypeptide chains two β polypeptide chains Hydrophobic R groups face inwards (toward centre) Helps maintain 3D shape Hydrophilic R groups face outwards Maintain solubility Each beta polypeptide chain has similar structure to myoglobin 4 inorganic prosthetic groups Haem (heme) group Contains Iron (Fe2+) ion Oxygen is very attracted to Iron (think rust) Function carry oxygen around in the blood Due to presence of haem group

One Complete Haemoglobin molecule 4 haem groups Each with one Fe2+ ion Carry 4 oxygen molecules (O2) Total of 8 oxygen atoms Haem group responsible for color of blood Purple NO oxygen with the Fe Red oxygen has combined with the Fe ion… “oxyhaemoglobin”

Sickle Cell Anemia One of the polar AA (glutamic acid) in the beta polypeptide chain is replaced with AA Valine (has a non-polar R group) Non-polar R group in the beta polypeptide chain (which is found on outside of molecule) makes haemoglobin much less soluble Causes clots RBC inefficient at delivering Oxygen “Anemia” is when there is a lower than normal RBC count Sickle RBC live only 10-20 day (normal RBCs live about 120) Bone marrow cannot replace fast enough

Collagen: Fibrous protein Structure Three polypeptide chains wound around each other Helical but NOT alpha helix (not tight enough) Every third AA is a glycine Collagen molecule=3 polypeptide chains wrapped around each other Hydrogen bonds form between these coils, which are around 1000 amino acids in length, which gives the structure strength (tensile strength) Collagen Molecule When 3 collagen peptide chains Collagen Fibrils When collagen molecules wrap around each other Collagen Fibres When many collagen fibrils wrap around each other Covalent cross links Form between R groups of lysines in the collagen molecules parallel to each other Holds together collagen fibres

Collagen functions Form the structure of bones Makes up cartilage and connective tissue Prevents blood that is being pumped at high pressure from bursting the walls of arteries Is the main component of tendons, which connect skeletal muscles to bones

Haemoglobin vs. Collagen Haemoglobin may be compared with Collagen as such: Basic Shape - Haemoglobin is globular while Collagen is fibrous Solubility - Haemoglobin is soluble in water while Collagen is insoluble Amino Acid Constituents - Haemoglobin contains a wide range of amino acids while Collagen has 35% of it primary structure made up of Glycine Prosthetic Group - Haemoglobin contains a haem prosthetic group while Collagen doesn't possess a prosthetic group Tertiary Structure - Much of the Haemoglobin molecule is wound into α helices while much of the Collagen molecule is made up of left handed helix structures

Testing For Proteins Biuret Test to show the presence of peptide bonds basis for the formation of proteins.  Peptide bonds will make the blue Biuret reagent turn purple.  This color change is dependent on the number of peptide bonds in the solution more protein, the more intense the change = longer polypeptide chain Procedures Create a control for the protein test (water and Biurets reagent) Add 5 mL of protein solution into test tube Add 5 drops of Biurets Reagent (very basic so do NOT get on hands or clothing) Gently shake/roll test tube between your hands Record color changes

Practice Set 4 Grading C D A B